ggsequence

Perform sequence alignment and render the results as a ggplot

library(ggplot2)
library(ggsequence)

Preparing the alignment

We need to make sure the alignment that we want to plot comes in the right format, which is as a MsaAAMultipleAlignment, with the original sequences as an attribute on the object

do_alignment = function(sequences) {
	# Make sure sequences have a name
	if (is.null(names(sequences))) {
		names(sequences) = as.character(1:length(sequences))
	}
	# Convert each of the sequence strings to a Biostrings::Views
	seqs = lapply( 1:length(sequences), function(seq_id) {
		views = Biostrings::Views(sequences[seq_id],start=1,end=nchar(sequences[seq_id]))
		names(views) = names(sequences)[seq_id]
		views
	})
	names(seqs) = names(sequences)

	# Perform the MSA on the sequences

	aln = msa::msaClustalOmega( Reduce(c,Map(function(view) { as(view,'AAStringSet')}, seqs)) )

	# Assign the original Views object to the sequences attribute
	attributes(aln)$sequences = seqs
	aln
}

Now, we can perform an alignment between two sequences, and plot them

p = ggplot(do_alignment(c(foo='MNTTTMMMNPPPPMNTTTMMMNPPPPMNTTTMMMNPPPPMNTTTMMMNPPPP',bar='NNSMMMPPNNSMMMPPNNSMMMPPNNSMMMPP')))
p

Which won't really give us anything useful apart from labels for the sequences and amino acid position. We can add in the sequence.

p + geom_text(aes(label=after_stat(aa)))

Or, we could add in the sequence, but colour the sequence based upon the conservation of the amino acid using the conservation stat.

p + geom_text(aes(label=after_stat(aa),color=after_stat(conservation),),stat="conservation")

Or, if we want a quick ClustalW style rendering of sequence

p + geom_text(aes(label=after_stat(aa))) + coord_conservation()

Which we could actually put on top of the sequence

p + geom_barcode()

Lets say we are only interested in the sequence that is aligned with another sequence - we can use the gappedSequence stat to draw segments

p + geom_text(aes(label=after_stat(aa))) + geom_segment(aes(x=after_stat(seqstart),xend=after_stat(seqend)),stat="gappedSequence",linewidth=2,colour="black",position = position_nudge(y=-0.1))

This is fine, but what if we want to map some data onto our aligned sequences? You can map on a data frame to the alignment using the alignedSite stat. You tell the stat where the data is (annotations parameter), and which column the sequence ids are in (id.column parameter), and which columns you want available as amino acid positions that have been rescaled to match the alignment - in this case start and end (columns parameter).

signalpeptide_data=data.frame(seq.ids=c('bar','foo'),start=c(1,1),end=c(3,4))
p + geom_text(aes(label=after_stat(aa))) + geom_segment(aes(x=after_stat(start),xend=after_stat(end)),stat="alignedSite",colour="red",size=4,alpha=0.5,annotations=signalpeptide_data,id.column='seq.ids',columns=c('start','end'))

Or, you can use some fancy brackets to indicate a region

p + geom_text(aes(label=after_stat(aa))) + geom_bracket(aes(x=after_stat(start),xend=after_stat(end)),offset=1,size=0.5,stat="alignedSite",annotations=signalpeptide_data,id.column='seq.ids',columns=c('start','end'))

If you have a data frame with specific annotations to add on, you can use the alignedSite stat to map that on to the sequences too

site_data = data.frame(seq.ids=c('bar','foo'),site=c(4,5))
site_data$site_label = as.character(site_data$site)
p + geom_text(aes(label=after_stat(aa))) + geom_point(aes(x=after_stat(site)),stat="alignedSite",annotations=site_data,id.column='seq.ids',columns=c('site'),position=position_nudge(y=0.1),color='red')

Extra columns get automatically made available within the geom, so if you have a column with labels for each row, you can easily access them.

p + geom_text(aes(label=after_stat(aa))) + geom_label(aes(x=after_stat(site),label=..site_label..),stat="alignedSite",annotations=site_data,id.column='seq.ids',columns=c('site'),position=position_nudge(y=0.1),color='red')

Or, if you are being really fancy

p + geom_text(aes(label=after_stat(aa))) + ggsugar::geom_sugar(aes(x=after_stat(site)),stat="alignedSite",annotations=site_data,id.column='seq.ids',columns=c('site'),position=position_nudge(y=0.1),size=10,sugar='gal(b1-3)galnac')

Or, if you are being EVEN fancier

site_data = data.frame(seq.ids=c('bar','foo'),site=c(4,5),sugarseq=c('man','gal(b1-3)galnac'))
p + geom_text(aes(label=after_stat(aa))) + ggsugar::geom_sugar(aes(x=after_stat(site),sugar=after_stat(sugarseq)),stat="alignedSite",annotations=site_data,id.column='seq.ids',columns=c('site'),position=position_nudge(y=0.1),size=5)